You should be able to rust proof a car with chipped paint so long as you are using the right product. If you are interested in applying the rust proofing to the undercarriage of the car, the chipped paint will have no effect. If you want to rust proof the exterior of the car, you should not apply it to an area that has chipped paint. Rust proofing solutions can damage the finish of all exterior paint, whether it is chipped or not. If there is chipped paint, you should touch it up or sand it off and repaint.